The RNA de novo structure modeling protocol. More...

#include <RNA_DeNovoProtocol.hh>

Inheritance diagram for protocols::rna::RNA_DeNovoProtocol:

Collaboration diagram for protocols::rna::RNA_DeNovoProtocol:

Public Member Functions
	RNA_DeNovoProtocol (Size const nstruct, std::string const silent_file, bool const heat_structure=true, bool const minimize_structure=false, bool const relax_structure=false, bool const allow_bulge=false)
	Construct the protocol object given the RNA fragment library to use. More...

	~RNA_DeNovoProtocol ()

virtual protocols::moves::MoverOP	clone () const
	Clone this object. More...

void	apply (core::pose::Pose &pose)
	Apply the RNA denovo modeling protocol to the input pose. More...

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	set_dump_pdb (bool const setting)

void	set_temperature (core::Real const setting)

void	set_jump_library_file (std::string const jump_library_file)

void	set_all_rna_fragments_file (std::string const file)

void	set_vall_torsions_file (std::string const file)

void	set_rna_params_file (std::string const file)

void	set_rna_data_file (std::string const file)

void	set_chunk_pdb_files (utility::vector1< std::string > const &chunk_pdb_files)

void	set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files)

void	set_input_res (utility::vector1< Size > const &input_res)

void	ignore_secstruct (bool const setting)

void	jump_change_frequency (core::Real const value)

void	set_close_loops (bool const setting)

void	set_close_loops_after_each_move (bool const setting)

void	simple_rmsd_cutoff_relax (bool const setting)

void	output_lores_silent_file (bool const setting)

void	set_filter_lores_base_pairs (bool const setting)

void	set_filter_lores_base_pairs_early (bool const setting)

void	set_filter_chain_closure (bool const setting)

void	set_filter_chain_closure_distance (core::Real const setting)

void	set_filter_chain_closure_halfway (bool const setting)

void	set_binary_rna_output (bool const setting)

void	set_suppress_bp_constraint (core::Real const setting)

void	set_lores_scorefxn (std::string const &lores_scorefxn)

void	set_vary_bond_geometry (bool const setting)

void	output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only=false) const

void	align_and_output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const

void	set_staged_constraints (bool const setting)

void	set_allow_consecutive_bulges (bool const setting)

void	set_chainbreak_weight (core::Real setting)

void	set_linear_chainbreak_weight (core::Real setting)

void	set_allowed_bulge_res (utility::vector1< core::Size > const &setting)

void	set_move_first_rigid_body (bool const setting)

void	set_root_at_first_rigid_body (bool const setting)

void	set_output_filters (bool const setting)

void	set_autofilter (bool const setting)

void	set_monte_carlo_cycles (Size const setting)

void	set_extra_minimize_res (utility::vector1< core::Size > setting)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	initialize_movers (core::pose::Pose &pose)

void	setup_monte_carlo_cycles (core::pose::Pose const &pose)

utility::vector1< Size >	get_moving_res (core::pose::Pose const &pose) const

void	initialize_lores_silent_file ()

void	initialize_constraints (core::pose::Pose &pose)

void	initialize_scorefxn (core::pose::Pose &pose)

void	initialize_tag_is_done ()

void	setup_rigid_body_mover (core::pose::Pose const &pose, core::Size const r, core::Size const rounds)

void	output_silent_struct (core::io::silent::SilentStruct &s, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, core::pose::Pose &pose, std::string const out_file_tag, bool const score_only=false) const

void	do_random_moves (core::pose::Pose &pose)

void	randomize_rigid_body_orientations (core::pose::Pose &pose)

void	update_denovo_scorefxn_weights (Size const &r, Size const &rounds)

Size	figure_out_constraint_separation_cutoff (Size const &r, Size const &rounds, Size const &max_dist)

void	update_pose_constraints (Size const &r, Size const &rounds, core::pose::Pose &pose)

void	update_frag_size (Size const &r, Size const &rounds)

void	random_fragment_trial (core::pose::Pose &pose)

bool	random_chunk_trial (core::pose::Pose &pose)

void	random_jump_trial (core::pose::Pose &pose)

void	RNA_move_trial (core::pose::Pose &pose)

void	add_number_base_pairs (core::pose::Pose const &pose_input, core::io::silent::SilentStruct &s) const

void	add_number_native_base_pairs (core::pose::Pose &pose, core::io::silent::SilentStruct &s) const

void	calc_rmsds (core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) const

bool	check_score_filter (core::Real const lores_score_, std::list< core::Real > &all_lores_score_)

void	apply_chem_shift_data (core::pose::Pose &pose, std::string const out_file_tag)

void	add_chem_shift_info (core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const

Private Attributes
Size const	nstruct_

Size	monte_carlo_cycles_

Size const	monte_carlo_cycles_max_default_

bool	user_defined_cycles_

std::string	all_rna_fragments_file_

std::string const	silent_file_

std::string	lores_silent_file_

bool const	heat_structure_

bool	dump_pdb_

bool const	minimize_structure_

bool const	relax_structure_

bool	ignore_secstruct_

bool	do_close_loops_

bool	close_loops_at_end_

bool	close_loops_in_last_round_

bool	close_loops_after_each_move_

bool	simple_rmsd_cutoff_relax_

bool	allow_bulge_

bool	allow_consecutive_bulges_

bool const	use_chem_shift_data_

core::Real	m_Temperature_

Size	frag_size_

protocols::moves::MonteCarloOP	monte_carlo_

protocols::rna::RNA_FragmentsOP	all_rna_fragments_

protocols::rna::RNA_FragmentMoverOP	rna_fragment_mover_

protocols::rna::RNA_LoopCloserOP	rna_loop_closer_

protocols::rna::RNA_ChunkLibraryOP	rna_chunk_library_

protocols::rna::RNA_MinimizerOP	rna_minimizer_

protocols::rna::RNA_RelaxerOP	rna_relaxer_

protocols::rigid::RigidBodyPerturbMoverOP	rigid_body_mover_

std::string	rna_params_file_

std::string	rna_data_file_

std::string	jump_library_file_

RNA_StructureParametersOP	rna_structure_parameters_

RNA_DataReaderOP	rna_data_reader_

bool	output_lores_silent_file_

bool	filter_lores_base_pairs_

bool	filter_lores_base_pairs_early_

bool	filter_chain_closure_

core::Real	filter_chain_closure_distance_

bool	filter_chain_closure_halfway_

bool	vary_bond_geometry_

bool	binary_rna_output_

core::scoring::constraints::ConstraintSetOP	constraint_set_

core::Real	jump_change_frequency_

std::map< std::string, bool >	tag_is_done_

std::string	lores_scorefxn_

core::scoring::ScoreFunctionOP	denovo_scorefxn_

core::scoring::ScoreFunctionOP	hires_scorefxn_

core::scoring::ScoreFunctionOP	chem_shift_scorefxn_

core::scoring::ScoreFunctionOP	initial_denovo_scorefxn_

core::scoring::rna::RNA_LowResolutionPotential	local_rna_low_resolution_potential_

utility::vector1< std::string >	chunk_pdb_files_

utility::vector1< std::string >	chunk_silent_files_

utility::vector1< core::Size >	input_res_

utility::vector1< core::Size >	allowed_bulge_res_

utility::vector1< core::Size >	extra_minimize_res_

core::Real	chunk_coverage_

bool	staged_constraints_

core::Real	chainbreak_weight_

core::Real	linear_chainbreak_weight_

bool	titrate_stack_bonus_

bool	move_first_rigid_body_

bool	root_at_first_rigid_body_

core::Real	suppress_bp_constraint_

bool	output_filters_

core::Real	lores_score_early_

core::Real	lores_score_final_

bool	autofilter_

core::Real	autofilter_score_quantile_

std::list< core::Real >	all_lores_score_final_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

The RNA de novo structure modeling protocol.

Definition at line 55 of file RNA_DeNovoProtocol.hh.

Constructor & Destructor Documentation

protocols::rna::RNA_DeNovoProtocol::RNA_DeNovoProtocol	(	Size const	nstruct,
		std::string const	silent_file,
		bool const	heat_structure = `true`,
		bool const	minimize_structure = `false`,
		bool const	relax_structure = `false`,
		bool const	allow_bulge = `false`
	)

Construct the protocol object given the RNA fragment library to use.

Definition at line 114 of file RNA_DeNovoProtocol.cc.

References local_rna_low_resolution_potential_, core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification(), and rna_loop_closer_.

Referenced by clone().

protocols::rna::RNA_DeNovoProtocol::~RNA_DeNovoProtocol ( )

Definition at line 186 of file RNA_DeNovoProtocol.cc.

Member Function Documentation

void protocols::rna::RNA_DeNovoProtocol::add_chem_shift_info	(	core::io::silent::SilentStruct &	silent_struct,
		core::pose::Pose const &	const_pose
	)		const

private

Definition at line 1236 of file RNA_DeNovoProtocol.cc.

References core::io::silent::SilentStruct::add_energy(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points(), core::io::silent::SilentStruct::has_energy(), core::scoring::rna_chem_shift, core::scoring::ScoreFunction::set_weight(), and use_chem_shift_data_.

Referenced by output_to_silent_file().

void protocols::rna::RNA_DeNovoProtocol::add_number_base_pairs	(	core::pose::Pose const &	pose_input,
		core::io::silent::SilentStruct &	s
	)		const

private

Definition at line 1013 of file RNA_DeNovoProtocol.cc.

References core::io::silent::SilentStruct::add_string_value(), protocols::rna::classify_base_pairs(), protocols::rna::get_number_base_stacks(), core::scoring::rna::possibly_canonical(), core::pose::Pose::residue(), and core::scoring::rna::WATSON_CRICK.

Referenced by output_silent_struct().

void protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs	(	core::pose::Pose &	pose,
		core::io::silent::SilentStruct &	s
	)		const

private

Definition at line 1100 of file RNA_DeNovoProtocol.cc.

Referenced by output_silent_struct().

void protocols::rna::RNA_DeNovoProtocol::align_and_output_to_silent_file	(	core::pose::Pose &	pose,
		std::string const &	silent_file,
		std::string const &	out_file_tag
	)		const

Definition at line 694 of file RNA_DeNovoProtocol.cc.

References protocols::swa::create_alignment_id_map(), get_moving_res(), protocols::moves::Mover::get_native_pose(), input_res_, output_to_silent_file(), rna_chunk_library_, core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::apply ( core::pose::Pose & pose)

virtual

Apply the RNA denovo modeling protocol to the input pose.

Apply the RNA de novo modeling protocol to a pose.

Implements protocols::moves::Mover.

Definition at line 192 of file RNA_DeNovoProtocol.cc.

References align_and_output_to_silent_file(), core::scoring::all_atom_rmsd(), all_lores_score_final_, allow_bulge_, allow_consecutive_bulges_, allowed_bulge_res_, apply_chem_shift_data(), autofilter_, check_score_filter(), chem_shift_scorefxn_, close_loops_after_each_move_, close_loops_at_end_, close_loops_in_last_round_, denovo_scorefxn_, do_close_loops_, do_random_moves(), core::io::pdb::dump_pdb(), core::pose::Pose::dump_pdb(), dump_pdb_, filter_chain_closure_, filter_chain_closure_distance_, filter_chain_closure_halfway_, filter_lores_base_pairs_, filter_lores_base_pairs_early_, frag_size_, protocols::moves::Mover::get_native_pose(), heat_structure_, hires_scorefxn_, initialize_lores_silent_file(), initialize_movers(), initialize_scorefxn(), initialize_tag_is_done(), lores_score_early_, lores_score_final_, lores_silent_file_, minimize_structure_, monte_carlo_, monte_carlo_cycles_, nstruct_, output_lores_silent_file_, relax_structure_, rna_chunk_library_, rna_loop_closer_, rna_minimizer_, RNA_move_trial(), rna_relaxer_, rna_structure_parameters_, setup_monte_carlo_cycles(), setup_rigid_body_mover(), silent_file_, tag_is_done_, protocols::rna::TR(), update_denovo_scorefxn_weights(), update_frag_size(), update_pose_constraints(), use_chem_shift_data_, and protocols::swa::rna::virtualize_bulges().

void protocols::rna::RNA_DeNovoProtocol::apply_chem_shift_data	(	core::pose::Pose &	pose,
		std::string const	out_file_tag
	)

private

Definition at line 1211 of file RNA_DeNovoProtocol.cc.

References chem_shift_scorefxn_, close_loops_at_end_, hires_scorefxn_, minimize_structure_, rna_loop_closer_, rna_minimizer_, rna_structure_parameters_, and use_chem_shift_data_.

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::calc_rmsds	(	core::io::silent::SilentStruct &	s,
		core::pose::Pose &	pose,
		std::string const &	out_file_tag
	)		const

private

Definition at line 587 of file RNA_DeNovoProtocol.cc.

References core::io::silent::SilentStruct::add_energy(), core::scoring::all_atom_rmsd(), protocols::moves::Mover::get_native_pose(), rna_structure_parameters_, and protocols::rna::TR().

Referenced by output_silent_struct().

bool protocols::rna::RNA_DeNovoProtocol::check_score_filter	(	core::Real const	lores_score_,
		std::list< core::Real > &	all_lores_score_
	)

private

Definition at line 1188 of file RNA_DeNovoProtocol.cc.

References autofilter_score_quantile_, and protocols::rna::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::rna::RNA_DeNovoProtocol::clone ( ) const

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

Definition at line 181 of file RNA_DeNovoProtocol.cc.

References RNA_DeNovoProtocol().

void protocols::rna::RNA_DeNovoProtocol::do_random_moves ( core::pose::Pose & pose)

private

Definition at line 732 of file RNA_DeNovoProtocol.cc.

References core::pose::Pose::dump_pdb(), dump_pdb_, randomize_rigid_body_orientations(), rna_chunk_library_, rna_fragment_mover_, core::pose::Pose::total_residue(), protocols::rna::TR(), and protocols::rna::translate_virtual_anchor_to_first_rigid_body().

Referenced by apply().

Size protocols::rna::RNA_DeNovoProtocol::figure_out_constraint_separation_cutoff	(	Size const &	r,
		Size const &	rounds,
		Size const &	max_dist
	)

private

Definition at line 838 of file RNA_DeNovoProtocol.cc.

Referenced by update_pose_constraints().

utility::vector1< Size > protocols::rna::RNA_DeNovoProtocol::get_moving_res ( core::pose::Pose const & pose) const

private

Definition at line 676 of file RNA_DeNovoProtocol.cc.

References rna_structure_parameters_, and core::pose::Pose::total_residue().

Referenced by align_and_output_to_silent_file(), and setup_monte_carlo_cycles().

std::string protocols::rna::RNA_DeNovoProtocol::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Definition at line 386 of file RNA_DeNovoProtocol.cc.

void protocols::rna::RNA_DeNovoProtocol::ignore_secstruct ( bool const setting)

inline

Definition at line 125 of file RNA_DeNovoProtocol.hh.

References ignore_secstruct_.

void protocols::rna::RNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose & pose)

private

Definition at line 429 of file RNA_DeNovoProtocol.cc.

References core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), constraint_set_, core::scoring::coordinate_constraint, and denovo_scorefxn_.

Referenced by initialize_scorefxn().

void protocols::rna::RNA_DeNovoProtocol::initialize_lores_silent_file ( )

private

Definition at line 571 of file RNA_DeNovoProtocol.cc.

References lores_silent_file_, output_lores_silent_file_, and silent_file_.

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::initialize_movers ( core::pose::Pose & pose)

private

void protocols::rna::RNA_DeNovoProtocol::initialize_scorefxn ( core::pose::Pose & pose)

private

Definition at line 393 of file RNA_DeNovoProtocol.cc.

References core::scoring::chainbreak, chainbreak_weight_, chem_shift_scorefxn_, core::scoring::ScoreFunctionFactory::create_score_function(), denovo_scorefxn_, hires_scorefxn_, initial_denovo_scorefxn_, initialize_constraints(), core::scoring::linear_chainbreak, linear_chainbreak_weight_, lores_scorefxn_, core::scoring::rna_chem_shift, rna_minimizer_, and use_chem_shift_data_.

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::initialize_tag_is_done ( )

private

Definition at line 517 of file RNA_DeNovoProtocol.cc.

References protocols::swa::rna::file_exists(), core::io::silent::SilentFileData::read_tags_fast(), silent_file_, and tag_is_done_.

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::jump_change_frequency ( core::Real const value)

inline

Definition at line 132 of file RNA_DeNovoProtocol.hh.

References jump_change_frequency_.

void protocols::rna::RNA_DeNovoProtocol::output_lores_silent_file ( bool const setting)

inline

Definition at line 147 of file RNA_DeNovoProtocol.hh.

References output_lores_silent_file_.

void protocols::rna::RNA_DeNovoProtocol::output_silent_struct	(	core::io::silent::SilentStruct &	s,
		core::io::silent::SilentFileData &	silent_file_data,
		std::string const &	silent_file,
		core::pose::Pose &	pose,
		std::string const	out_file_tag,
		bool const	score_only = `false`
	)		const

private

Definition at line 608 of file RNA_DeNovoProtocol.cc.

References core::io::silent::SilentStruct::add_energy(), add_number_base_pairs(), add_number_native_base_pairs(), calc_rmsds(), protocols::moves::Mover::get_native_pose(), lores_score_early_, lores_score_final_, minimize_structure_, output_filters_, protocols::rna::TR(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by output_to_silent_file().

void protocols::rna::RNA_DeNovoProtocol::output_to_silent_file	(	core::pose::Pose &	pose,
		std::string const &	silent_file,
		std::string const &	out_file_tag,
		bool const	score_only = `false`
	)		const

Definition at line 637 of file RNA_DeNovoProtocol.cc.

References add_chem_shift_info(), binary_rna_output_, output_silent_struct(), protocols::rna::TR(), and use_chem_shift_data_.

Referenced by align_and_output_to_silent_file().

bool protocols::rna::RNA_DeNovoProtocol::random_chunk_trial ( core::pose::Pose & pose)

private

Definition at line 984 of file RNA_DeNovoProtocol.cc.

References do_close_loops_, monte_carlo_, rna_chunk_library_, and rna_loop_closer_.

Referenced by RNA_move_trial().

void protocols::rna::RNA_DeNovoProtocol::random_fragment_trial ( core::pose::Pose & pose)

private

Definition at line 973 of file RNA_DeNovoProtocol.cc.

References do_close_loops_, frag_size_, monte_carlo_, rna_fragment_mover_, and rna_loop_closer_.

Referenced by RNA_move_trial().

void protocols::rna::RNA_DeNovoProtocol::random_jump_trial ( core::pose::Pose & pose)

private

Definition at line 938 of file RNA_DeNovoProtocol.cc.

References do_close_loops_, monte_carlo_, protocols::rna::RG(), rigid_body_mover_, rna_loop_closer_, and rna_structure_parameters_.

Referenced by RNA_move_trial().

void protocols::rna::RNA_DeNovoProtocol::randomize_rigid_body_orientations ( core::pose::Pose & pose)

private

Definition at line 764 of file RNA_DeNovoProtocol.cc.

References protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rna::get_rigid_body_jumps(), core::kinematics::Jump::get_translation(), core::pose::Pose::jump(), protocols::rigid::partner_upstream, core::pose::Pose::set_jump(), and core::kinematics::Jump::set_translation().

Referenced by do_random_moves().

void protocols::rna::RNA_DeNovoProtocol::RNA_move_trial ( core::pose::Pose & pose)

private

Definition at line 907 of file RNA_DeNovoProtocol.cc.

References chunk_coverage_, jump_change_frequency_, random_chunk_trial(), random_fragment_trial(), random_jump_trial(), and protocols::rna::RG().

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::set_all_rna_fragments_file ( std::string const file)

inline

Definition at line 90 of file RNA_DeNovoProtocol.hh.

References all_rna_fragments_file_.

void protocols::rna::RNA_DeNovoProtocol::set_allow_consecutive_bulges ( bool const setting)

inline

Definition at line 192 of file RNA_DeNovoProtocol.hh.

References allow_consecutive_bulges_.

void protocols::rna::RNA_DeNovoProtocol::set_allowed_bulge_res ( utility::vector1< core::Size > const & setting)

inline

Definition at line 201 of file RNA_DeNovoProtocol.hh.

References allowed_bulge_res_.

void protocols::rna::RNA_DeNovoProtocol::set_autofilter ( bool const setting)

inline

Definition at line 213 of file RNA_DeNovoProtocol.hh.

References autofilter_.

void protocols::rna::RNA_DeNovoProtocol::set_binary_rna_output ( bool const setting)

inline

Definition at line 168 of file RNA_DeNovoProtocol.hh.

References binary_rna_output_.

void protocols::rna::RNA_DeNovoProtocol::set_chainbreak_weight ( core::Real setting)

inline

Definition at line 195 of file RNA_DeNovoProtocol.hh.

References chainbreak_weight_.

void protocols::rna::RNA_DeNovoProtocol::set_chunk_pdb_files ( utility::vector1< std::string > const & chunk_pdb_files)

inline

Definition at line 110 of file RNA_DeNovoProtocol.hh.

References chunk_pdb_files_.

void protocols::rna::RNA_DeNovoProtocol::set_chunk_silent_files ( utility::vector1< std::string > const & chunk_silent_files)

inline

Definition at line 115 of file RNA_DeNovoProtocol.hh.

References chunk_silent_files_.

void protocols::rna::RNA_DeNovoProtocol::set_close_loops ( bool const setting)

inline

Definition at line 135 of file RNA_DeNovoProtocol.hh.

References binary_rna_output_, and close_loops_at_end_.

void protocols::rna::RNA_DeNovoProtocol::set_close_loops_after_each_move ( bool const setting)

inline

Definition at line 141 of file RNA_DeNovoProtocol.hh.

References close_loops_after_each_move_.

void protocols::rna::RNA_DeNovoProtocol::set_dump_pdb ( bool const setting)

inline

Definition at line 79 of file RNA_DeNovoProtocol.hh.

References dump_pdb_.

void protocols::rna::RNA_DeNovoProtocol::set_extra_minimize_res ( utility::vector1< core::Size > setting)

Definition at line 1182 of file RNA_DeNovoProtocol.cc.

References extra_minimize_res_.

void protocols::rna::RNA_DeNovoProtocol::set_filter_chain_closure ( bool const setting)

inline

Definition at line 159 of file RNA_DeNovoProtocol.hh.

References filter_chain_closure_.

void protocols::rna::RNA_DeNovoProtocol::set_filter_chain_closure_distance ( core::Real const setting)

inline

Definition at line 162 of file RNA_DeNovoProtocol.hh.

References filter_chain_closure_distance_.

void protocols::rna::RNA_DeNovoProtocol::set_filter_chain_closure_halfway ( bool const setting)

inline

Definition at line 165 of file RNA_DeNovoProtocol.hh.

References filter_chain_closure_halfway_.

void protocols::rna::RNA_DeNovoProtocol::set_filter_lores_base_pairs ( bool const setting)

inline

Definition at line 150 of file RNA_DeNovoProtocol.hh.

References filter_lores_base_pairs_.

void protocols::rna::RNA_DeNovoProtocol::set_filter_lores_base_pairs_early ( bool const setting)

inline

Definition at line 153 of file RNA_DeNovoProtocol.hh.

References filter_lores_base_pairs_, and filter_lores_base_pairs_early_.

void protocols::rna::RNA_DeNovoProtocol::set_input_res ( utility::vector1< Size > const & input_res)

inline

Definition at line 120 of file RNA_DeNovoProtocol.hh.

References input_res_.

void protocols::rna::RNA_DeNovoProtocol::set_jump_library_file ( std::string const jump_library_file)

inline

Definition at line 85 of file RNA_DeNovoProtocol.hh.

References jump_library_file_.

void protocols::rna::RNA_DeNovoProtocol::set_linear_chainbreak_weight ( core::Real setting)

inline

Definition at line 198 of file RNA_DeNovoProtocol.hh.

References linear_chainbreak_weight_.

void protocols::rna::RNA_DeNovoProtocol::set_lores_scorefxn ( std::string const & lores_scorefxn)

inline

Definition at line 174 of file RNA_DeNovoProtocol.hh.

References lores_scorefxn_.

void protocols::rna::RNA_DeNovoProtocol::set_monte_carlo_cycles ( Size const setting)

inline

Definition at line 216 of file RNA_DeNovoProtocol.hh.

References monte_carlo_cycles_, and user_defined_cycles_.

void protocols::rna::RNA_DeNovoProtocol::set_move_first_rigid_body ( bool const setting)

inline

Definition at line 204 of file RNA_DeNovoProtocol.hh.

References move_first_rigid_body_.

void protocols::rna::RNA_DeNovoProtocol::set_output_filters ( bool const setting)

inline

Definition at line 210 of file RNA_DeNovoProtocol.hh.

References output_filters_.

void protocols::rna::RNA_DeNovoProtocol::set_rna_data_file ( std::string const file)

inline

Definition at line 105 of file RNA_DeNovoProtocol.hh.

References rna_data_file_.

void protocols::rna::RNA_DeNovoProtocol::set_rna_params_file ( std::string const file)

inline

Definition at line 100 of file RNA_DeNovoProtocol.hh.

References rna_params_file_.

void protocols::rna::RNA_DeNovoProtocol::set_root_at_first_rigid_body ( bool const setting)

inline

Definition at line 207 of file RNA_DeNovoProtocol.hh.

References root_at_first_rigid_body_.

void protocols::rna::RNA_DeNovoProtocol::set_staged_constraints ( bool const setting)

inline

Definition at line 189 of file RNA_DeNovoProtocol.hh.

References staged_constraints_.

void protocols::rna::RNA_DeNovoProtocol::set_suppress_bp_constraint ( core::Real const setting)

inline

Definition at line 171 of file RNA_DeNovoProtocol.hh.

References suppress_bp_constraint_.

void protocols::rna::RNA_DeNovoProtocol::set_temperature ( core::Real const setting)

inline

Definition at line 82 of file RNA_DeNovoProtocol.hh.

References m_Temperature_.

void protocols::rna::RNA_DeNovoProtocol::set_vall_torsions_file ( std::string const file)

inline

Definition at line 95 of file RNA_DeNovoProtocol.hh.

References all_rna_fragments_file_.

void protocols::rna::RNA_DeNovoProtocol::set_vary_bond_geometry ( bool const setting)

inline

Definition at line 177 of file RNA_DeNovoProtocol.hh.

References binary_rna_output_, and vary_bond_geometry_.

void protocols::rna::RNA_DeNovoProtocol::setup_monte_carlo_cycles ( core::pose::Pose const & pose)

private

Definition at line 489 of file RNA_DeNovoProtocol.cc.

References get_moving_res(), protocols::rna::get_rigid_body_jumps(), monte_carlo_cycles_, monte_carlo_cycles_max_default_, protocols::rna::TR(), and user_defined_cycles_.

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::setup_rigid_body_mover	(	core::pose::Pose const &	pose,
		core::Size const	r,
		core::Size const	rounds
	)

private

Definition at line 541 of file RNA_DeNovoProtocol.cc.

References binary_rna_output_, jump_change_frequency_, protocols::rna::let_rigid_body_jumps_move(), move_first_rigid_body_, protocols::rigid::partner_upstream, rigid_body_mover_, core::kinematics::MoveMap::set_jump(), and protocols::rna::TR().

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax ( bool const setting)

inline

Definition at line 144 of file RNA_DeNovoProtocol.hh.

References simple_rmsd_cutoff_relax_.

void protocols::rna::RNA_DeNovoProtocol::update_denovo_scorefxn_weights	(	Size const &	r,
		Size const &	rounds
	)

private

Definition at line 802 of file RNA_DeNovoProtocol.cc.

References core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::coordinate_constraint, denovo_scorefxn_, initial_denovo_scorefxn_, core::scoring::linear_chainbreak, core::scoring::rna_base_axis, core::scoring::rna_base_stack_axis, core::scoring::rna_base_stagger, and titrate_stack_bonus_.

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::update_frag_size	(	Size const &	r,
		Size const &	rounds
	)

private

Definition at line 896 of file RNA_DeNovoProtocol.cc.

References frag_size_, and protocols::rna::TR().

Referenced by apply().

void protocols::rna::RNA_DeNovoProtocol::update_pose_constraints	(	Size const &	r,
		Size const &	rounds,
		core::pose::Pose &	pose
	)

private

Definition at line 854 of file RNA_DeNovoProtocol.cc.

References core::pose::Pose::constraint_set(), constraint_set_, figure_out_constraint_separation_cutoff(), core::pose::Pose::fold_tree(), staged_constraints_, and protocols::rna::TR().

Referenced by apply().

Member Data Documentation

std::list< core::Real > protocols::rna::RNA_DeNovoProtocol::all_lores_score_final_

private

Definition at line 397 of file RNA_DeNovoProtocol.hh.

Referenced by apply().

protocols::rna::RNA_FragmentsOP protocols::rna::RNA_DeNovoProtocol::all_rna_fragments_

private

Definition at line 336 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers().

std::string protocols::rna::RNA_DeNovoProtocol::all_rna_fragments_file_

private

Definition at line 311 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), set_all_rna_fragments_file(), and set_vall_torsions_file().

bool protocols::rna::RNA_DeNovoProtocol::allow_bulge_

private

Definition at line 326 of file RNA_DeNovoProtocol.hh.

Referenced by apply().

bool protocols::rna::RNA_DeNovoProtocol::allow_consecutive_bulges_

private

Definition at line 326 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_allow_consecutive_bulges().

utility::vector1< core::Size > protocols::rna::RNA_DeNovoProtocol::allowed_bulge_res_

private

Definition at line 378 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_allowed_bulge_res().

bool protocols::rna::RNA_DeNovoProtocol::autofilter_

private

Definition at line 395 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_autofilter().

core::Real protocols::rna::RNA_DeNovoProtocol::autofilter_score_quantile_

private

Definition at line 396 of file RNA_DeNovoProtocol.hh.

Referenced by check_score_filter().

bool protocols::rna::RNA_DeNovoProtocol::binary_rna_output_

private

Definition at line 361 of file RNA_DeNovoProtocol.hh.

Referenced by output_to_silent_file(), set_binary_rna_output(), set_close_loops(), set_vary_bond_geometry(), and setup_rigid_body_mover().

core::Real protocols::rna::RNA_DeNovoProtocol::chainbreak_weight_

private

Definition at line 384 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_scorefxn(), and set_chainbreak_weight().

core::scoring::ScoreFunctionOP protocols::rna::RNA_DeNovoProtocol::chem_shift_scorefxn_

private

Definition at line 371 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), and initialize_scorefxn().

core::Real protocols::rna::RNA_DeNovoProtocol::chunk_coverage_

private

Definition at line 380 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and RNA_move_trial().

utility::vector1< std::string > protocols::rna::RNA_DeNovoProtocol::chunk_pdb_files_

private

Definition at line 375 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_chunk_pdb_files().

utility::vector1< std::string > protocols::rna::RNA_DeNovoProtocol::chunk_silent_files_

private

Definition at line 376 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_chunk_silent_files().

bool protocols::rna::RNA_DeNovoProtocol::close_loops_after_each_move_

private

Definition at line 323 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_close_loops_after_each_move().

bool protocols::rna::RNA_DeNovoProtocol::close_loops_at_end_

private

Definition at line 321 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), and set_close_loops().

bool protocols::rna::RNA_DeNovoProtocol::close_loops_in_last_round_

private

Definition at line 322 of file RNA_DeNovoProtocol.hh.

Referenced by apply().

core::scoring::constraints::ConstraintSetOP protocols::rna::RNA_DeNovoProtocol::constraint_set_

private

Definition at line 363 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_constraints(), and update_pose_constraints().

core::scoring::ScoreFunctionOP protocols::rna::RNA_DeNovoProtocol::denovo_scorefxn_

private

Definition at line 370 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), initialize_constraints(), initialize_scorefxn(), and update_denovo_scorefxn_weights().

bool protocols::rna::RNA_DeNovoProtocol::do_close_loops_

private

Definition at line 320 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), random_chunk_trial(), random_fragment_trial(), and random_jump_trial().

bool protocols::rna::RNA_DeNovoProtocol::dump_pdb_

private

Definition at line 315 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), do_random_moves(), and set_dump_pdb().

utility::vector1< core::Size > protocols::rna::RNA_DeNovoProtocol::extra_minimize_res_

private

Definition at line 379 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_extra_minimize_res().

bool protocols::rna::RNA_DeNovoProtocol::filter_chain_closure_

private

Definition at line 356 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_filter_chain_closure().

core::Real protocols::rna::RNA_DeNovoProtocol::filter_chain_closure_distance_

private

Definition at line 357 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_filter_chain_closure_distance().

bool protocols::rna::RNA_DeNovoProtocol::filter_chain_closure_halfway_

private

Definition at line 358 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_filter_chain_closure_halfway().

bool protocols::rna::RNA_DeNovoProtocol::filter_lores_base_pairs_

private

Definition at line 353 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), set_filter_lores_base_pairs(), and set_filter_lores_base_pairs_early().

bool protocols::rna::RNA_DeNovoProtocol::filter_lores_base_pairs_early_

private

Definition at line 354 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and set_filter_lores_base_pairs_early().

Size protocols::rna::RNA_DeNovoProtocol::frag_size_

private

Definition at line 332 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), random_fragment_trial(), and update_frag_size().

bool const protocols::rna::RNA_DeNovoProtocol::heat_structure_

private

Definition at line 314 of file RNA_DeNovoProtocol.hh.

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::rna::RNA_DeNovoProtocol::hires_scorefxn_

private

Definition at line 370 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), and initialize_scorefxn().

bool protocols::rna::RNA_DeNovoProtocol::ignore_secstruct_

private

Definition at line 318 of file RNA_DeNovoProtocol.hh.

Referenced by ignore_secstruct(), and initialize_movers().

core::scoring::ScoreFunctionOP protocols::rna::RNA_DeNovoProtocol::initial_denovo_scorefxn_

private

Definition at line 372 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_scorefxn(), and update_denovo_scorefxn_weights().

utility::vector1< core::Size > protocols::rna::RNA_DeNovoProtocol::input_res_

private

Definition at line 377 of file RNA_DeNovoProtocol.hh.

Referenced by align_and_output_to_silent_file(), initialize_movers(), and set_input_res().

core::Real protocols::rna::RNA_DeNovoProtocol::jump_change_frequency_

private

Definition at line 365 of file RNA_DeNovoProtocol.hh.

Referenced by jump_change_frequency(), RNA_move_trial(), and setup_rigid_body_mover().

std::string protocols::rna::RNA_DeNovoProtocol::jump_library_file_

private

Definition at line 346 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_jump_library_file().

core::Real protocols::rna::RNA_DeNovoProtocol::linear_chainbreak_weight_

private

Definition at line 385 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_scorefxn(), and set_linear_chainbreak_weight().

core::scoring::rna::RNA_LowResolutionPotential protocols::rna::RNA_DeNovoProtocol::local_rna_low_resolution_potential_

private

Definition at line 373 of file RNA_DeNovoProtocol.hh.

Referenced by RNA_DeNovoProtocol().

core::Real protocols::rna::RNA_DeNovoProtocol::lores_score_early_

private

Definition at line 393 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and output_silent_struct().

core::Real protocols::rna::RNA_DeNovoProtocol::lores_score_final_

private

Definition at line 394 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and output_silent_struct().

std::string protocols::rna::RNA_DeNovoProtocol::lores_scorefxn_

private

Definition at line 369 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_scorefxn(), and set_lores_scorefxn().

std::string protocols::rna::RNA_DeNovoProtocol::lores_silent_file_

private

Definition at line 313 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and initialize_lores_silent_file().

core::Real protocols::rna::RNA_DeNovoProtocol::m_Temperature_

private

Definition at line 331 of file RNA_DeNovoProtocol.hh.

Referenced by set_temperature().

bool const protocols::rna::RNA_DeNovoProtocol::minimize_structure_

private

Definition at line 316 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), and output_silent_struct().

protocols::moves::MonteCarloOP protocols::rna::RNA_DeNovoProtocol::monte_carlo_

private

Definition at line 334 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), random_chunk_trial(), random_fragment_trial(), and random_jump_trial().

Size protocols::rna::RNA_DeNovoProtocol::monte_carlo_cycles_

private

Definition at line 308 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), set_monte_carlo_cycles(), and setup_monte_carlo_cycles().

Size const protocols::rna::RNA_DeNovoProtocol::monte_carlo_cycles_max_default_

private

Definition at line 309 of file RNA_DeNovoProtocol.hh.

Referenced by setup_monte_carlo_cycles().

bool protocols::rna::RNA_DeNovoProtocol::move_first_rigid_body_

private

Definition at line 388 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), set_move_first_rigid_body(), and setup_rigid_body_mover().

Size const protocols::rna::RNA_DeNovoProtocol::nstruct_

private

Definition at line 307 of file RNA_DeNovoProtocol.hh.

Referenced by apply().

bool protocols::rna::RNA_DeNovoProtocol::output_filters_

private

Definition at line 392 of file RNA_DeNovoProtocol.hh.

Referenced by output_silent_struct(), and set_output_filters().

bool protocols::rna::RNA_DeNovoProtocol::output_lores_silent_file_

private

Definition at line 351 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), initialize_lores_silent_file(), and output_lores_silent_file().

bool const protocols::rna::RNA_DeNovoProtocol::relax_structure_

private

Definition at line 317 of file RNA_DeNovoProtocol.hh.

Referenced by apply().

protocols::rigid::RigidBodyPerturbMoverOP protocols::rna::RNA_DeNovoProtocol::rigid_body_mover_

private

Definition at line 342 of file RNA_DeNovoProtocol.hh.

Referenced by random_jump_trial(), and setup_rigid_body_mover().

protocols::rna::RNA_ChunkLibraryOP protocols::rna::RNA_DeNovoProtocol::rna_chunk_library_

private

Definition at line 339 of file RNA_DeNovoProtocol.hh.

Referenced by align_and_output_to_silent_file(), apply(), do_random_moves(), initialize_movers(), and random_chunk_trial().

std::string protocols::rna::RNA_DeNovoProtocol::rna_data_file_

private

Definition at line 345 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_rna_data_file().

RNA_DataReaderOP protocols::rna::RNA_DeNovoProtocol::rna_data_reader_

private

Definition at line 349 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers().

protocols::rna::RNA_FragmentMoverOP protocols::rna::RNA_DeNovoProtocol::rna_fragment_mover_

private

Definition at line 337 of file RNA_DeNovoProtocol.hh.

Referenced by do_random_moves(), initialize_movers(), and random_fragment_trial().

protocols::rna::RNA_LoopCloserOP protocols::rna::RNA_DeNovoProtocol::rna_loop_closer_

private

Definition at line 338 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), random_chunk_trial(), random_fragment_trial(), random_jump_trial(), and RNA_DeNovoProtocol().

protocols::rna::RNA_MinimizerOP protocols::rna::RNA_DeNovoProtocol::rna_minimizer_

private

Definition at line 340 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), initialize_movers(), and initialize_scorefxn().

std::string protocols::rna::RNA_DeNovoProtocol::rna_params_file_

private

Definition at line 344 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_rna_params_file().

protocols::rna::RNA_RelaxerOP protocols::rna::RNA_DeNovoProtocol::rna_relaxer_

private

Definition at line 341 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and initialize_movers().

RNA_StructureParametersOP protocols::rna::RNA_DeNovoProtocol::rna_structure_parameters_

private

Definition at line 348 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), apply_chem_shift_data(), calc_rmsds(), get_moving_res(), initialize_movers(), and random_jump_trial().

bool protocols::rna::RNA_DeNovoProtocol::root_at_first_rigid_body_

private

Definition at line 389 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_root_at_first_rigid_body().

std::string const protocols::rna::RNA_DeNovoProtocol::silent_file_

private

Definition at line 312 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), initialize_lores_silent_file(), and initialize_tag_is_done().

bool protocols::rna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax_

private

Definition at line 325 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and simple_rmsd_cutoff_relax().

bool protocols::rna::RNA_DeNovoProtocol::staged_constraints_

private

Definition at line 382 of file RNA_DeNovoProtocol.hh.

Referenced by set_staged_constraints(), and update_pose_constraints().

core::Real protocols::rna::RNA_DeNovoProtocol::suppress_bp_constraint_

private

Definition at line 390 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_suppress_bp_constraint().

std::map< std::string, bool > protocols::rna::RNA_DeNovoProtocol::tag_is_done_

private

Definition at line 367 of file RNA_DeNovoProtocol.hh.

Referenced by apply(), and initialize_tag_is_done().

bool protocols::rna::RNA_DeNovoProtocol::titrate_stack_bonus_

private

Definition at line 387 of file RNA_DeNovoProtocol.hh.

Referenced by update_denovo_scorefxn_weights().

bool const protocols::rna::RNA_DeNovoProtocol::use_chem_shift_data_

private

Definition at line 328 of file RNA_DeNovoProtocol.hh.

Referenced by add_chem_shift_info(), apply(), apply_chem_shift_data(), initialize_scorefxn(), and output_to_silent_file().

bool protocols::rna::RNA_DeNovoProtocol::user_defined_cycles_

private

Definition at line 310 of file RNA_DeNovoProtocol.hh.

Referenced by set_monte_carlo_cycles(), and setup_monte_carlo_cycles().

bool protocols::rna::RNA_DeNovoProtocol::vary_bond_geometry_

private

Definition at line 360 of file RNA_DeNovoProtocol.hh.

Referenced by initialize_movers(), and set_vary_bond_geometry().

The documentation for this class was generated from the following files:

src/protocols/rna/RNA_DeNovoProtocol.hh
src/protocols/rna/RNA_DeNovoProtocol.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation